http://imagej.273.s1.nabble.com/Radial-distribution-function-tp5015874p5015899.html
> Hi Serhiy,
>
> below is a RDF macro (not the very latest version, I fear). Note that it
> is for 2D RDFs; if you are interested in 3D RDFs you need a correction that
> depends on the size of the particles.
>
> You need the "Radial Profile" plugin,
>
http://rsb.info.nih.gov/ij/plugins/radial-profile.html>
> An alternative would be finding the centroids with "Analyze Particles" and
> running a loop that determines all the difference vectors between pairs of
> particles.
>
> Michael
> ________________________________________________________________
> On Mar 13, 2016, at 22:57, Serhiy Malynych wrote:
>
> > Hi,
> >
> > I need to determine radial distribution function of nanoparticles from
> SEM
> > image. There are references in the Internet at imagejdocu.tudor.lu
> regarding
> > macro by Michael Schmid, but the link seems to be old and doesn't open. I
> > did install Radial Profile Plot plugin from ImageJ web-site but I'm not
> > sure this is exactly what I need. Can anyone help on that matter.
> >
> > Thanks,
> > Serhiy
> ________________________________________________________________
>
> // ImageJ macro to calculate the Radial Distribution Function (RDF)
> //
> // Use with a binary input image having black particles on white background
> // Needs the "Radial Profile" plugin,
>
http://rsb.info.nih.gov/ij/plugins/radial-profile.html> //
> // Limitations:
> // - Particle positions are rounded to nearest full pixel.
> // - Distance is in pixels, irrespective of any spatial calibration of the
> image
> //
> // Version: 2008-Dec-04 Michael Schmid
> //
> setBatchMode(true);
> width=getWidth;
> height=getHeight;
> //maxRadius may be modified, should not be larger than 0.3*minOf(width,
> height);
> maxRadius=0.3*minOf(width, height);
> minFFTsize=1.3*maxOf(width, height);
> title=getTitle();
> //make autocorrelation of particle positions
> size=4;
> while(size<minFFTsize) size*=2;
> run("Find Maxima...", "noise=10 output=[Single Points] light exclude");
> tempID=getImageID();
> tempTitle="temp-"+random();
> rename(tempTitle);
> run("Canvas Size...", "width="+ size+" height="+ size+" position=Center
> zero");
> run("FD Math...", "image1=["+tempTitle+"] operation=Correlate
> image2=["+tempTitle+"] result=AutoCorrelation do");
> psID=getImageID();
> selectImage(tempID);
> close();
>
> //make autocorrelation reference to correct finite image size effects
> newImage("frame", "8-bit White", width, height, 1);
> run("Set...", "value=255");
> tempID=getImageID();
> rename(tempTitle);
> run("Canvas Size...", "width="+ size+" height="+ size+" position=Center
> zero");
> run("FD Math...", "image1=["+tempTitle+"] operation=Correlate
> image2=["+tempTitle+"] result=AutoCorrReference do");
> refID=getImageID();
> imageCalculator("Divide", psID,refID);
> selectImage(refID);
> close();
> selectImage(tempID);
> close();
>
> //prepare normalized power spectrum for radial averaging
> selectImage(psID);
> makeRectangle(size/2, size/2, 1, 1);
> run("Set...", "value=0");
> run("Select None");
> circleSize=2*floor(maxRadius)+1;
> run("Specify...", "width="+circleSize+" height="+circleSize+"
> x="+(size/2+0.5)+" y="+(size/2+0.5)+" oval centered");
> getRawStatistics(nPixels, mean);
> run("Select None");
> run("Divide...", "value="+mean);
> run("Specify...", "width="+circleSize+" height="+circleSize+"
> x="+(size/2+0.5)+" y="+(size/2+0.5)+" oval centered");
> run("Radial Profile", "x="+(size/2+0.5)+" y="+(size/2+0.5)+"
> radius="+floor(maxRadius)-1);
> rename("RDF of "+title);
> selectImage(psID);
> close();
> setBatchMode("exit and display");
>
> --
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